This is just an idea, so feel free to use/add to it. It's from one of the planned (but abandoned) features of Obi-Wan (back when it was still for the PC).

Map:

Theed Courtyard (with walls and statues and things to take cover behind, fountains, anything else that makes it look like it fits in the movie). Connects to the "main gate" or something similar that enters the palace, plus various stairways and elevators leading to rooms and finally the Queen's inner chamber.

Teams:

Trade Federation (Red) vs. Naboo guard (Blue)

Trade Federation Objectives:

1) Destroy communications array. Have some kind of sattelite-like station or reactor that needs to be destroyed, preventing the Naboo from calling for help. This could be in a nearby building, or just outside the palace courtyard (like a power station). Perhaps there are STAPs available and maybe a Trade Fed tank they can use, sort of like how Hoth starts.

2) Break into the palace. I'm thinking they start in the courtyard outside the palace and have to blast their way through a wall or two.

3) Get past security. This would entail either using Techs to hack through certain access panels en route to the main audience chamber or else blasting through certain doors using heavy weapons and explosive charges.

4) Secure Hanger. Not sure about the order of this objective with the others, but somewhere along the line it would be logical for the Trade Federation to secure the ship hanger to prevent the Naboo from using them to escape. "Securing" could simply involve entering the hanger and hitting a switch or two (closing and locking the doors that lead outside).

Perhaps an alternate way to complete this objective could be to blow up all the ships in the hangar (there couldn't be too many), through use of explosives. The switches would be hack switches rather than normal switches, since the Naboo would have locked out the security codes. Or perhaps you could throw in another scenario like having to grab a droid's head to get the codes like in Hoth, but I didn't want to totally copy that scenario, good as it was.

5) Capture the Queen. That line by the battle droid in the Phantom Menace always makes me think of a game objective "We have captured the Queen!" ; )

I figure the Queen could just be an NPC with no weapons who is in a room near the end. Once that room is breached and you walk up to her, the mission ends. Or perhaps if she is killed (open the door and start shooting) the mission would also end. The room she's in could have a door that needs hacking/blasting and could be guarded by security lasers inside (programmable by Techs). As a last ditch effort you could have a Jedi stand in front of her with his saber out to protect her in the small room.

The Naboo objectives would simply be to stop the Trade Federation from accomplishing these goals within the time limit (20 mins, 30 mins whatever it is).

Suggested Classes:

Trade Federation:

Assault
Battle Droid Infantry: Standard Battle Droid we all known and love from TPM. Give him a "droid blaster" (more or less the same as an ST Rifle), repeater, fists, and blastech (or Episode I equivalent). The weapons are less important, and could be balanced to the map.

Heavy Weapons
Destroyer Droid (droideka). Make his "shield" a temporary use item that recharges much like the Cloak or Jetpack. Have him be forced into stationary mode while using it, but can still fire (can turn?). walking he should be very slow, rolling he should be faster. Stop to fire. Should his internal guns use ammo? Or should they just "recharge" over time (and be instantly recharged by Techs). The regular droids should certainly use ammo. Not sure about other weapons. Melee would be his slow clumsy (powerful?) fists (whatever those things are that pass for limbs).

Alternately this class could just be another Battle Droid with Merr Sonn, but we have so many already.

Scout
Probe Droid. Just for fun, make him look like one of those "Sith" probe droids Darth Maul used to track Qui-Gon & Co. on Tatooine (since I don't know what the Trade Fed. counterpart would be). Make it float, but large (perhaps the size of those "sentry" droids that you fight in JA and JK2 single player... not to be confused with the placeable assault sentries). Perhaps it could have a temporary cloaking device (like Lando has). It could fly, but only hover a few feet off the ground and would have a blaster of some kind (silenced?). Additionally it could have a set of Macrobinoculars (the item is already there in the menu) and a Stun Baton. Weak health.

Tech
Droid Mechanic. He'd be able to "repair" other droids and hack through doors, as well as provide ammo, like most Techs. Perhaps the ability to drop a Sentry as well. Fast speed, low health.
I'm thinking a White battle droid with a red cross on him or something of that nature.

Jedi
Sith Lord: Darth Maul (of course) even though he wasn't involved in the capture he's the only Dark Jedi character that really fits. Give him a Saberstaff, and maybe Push and Jump, not sure about his other powers.

For audio sounds its not necessary, but some custom sounds like having the droid say "Roger Roger" would be nice touches. ; )